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- PDB-3sx6: Crystal structure of sulfide:quinone oxidoreductase Cys356Ala var... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3sx6 | |||||||||
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Title | Crystal structure of sulfide:quinone oxidoreductase Cys356Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone | |||||||||
![]() | Sulfide-quinone reductase | |||||||||
![]() | OXIDOREDUCTASE / sulfide:quinone oxidoreductase / Cys356Ala variant / integral monotopic membrane protein / complex with sulfide and decylubiquinone | |||||||||
Function / homology | ![]() bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / quinone binding / nucleotide binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cherney, M.M. / Zhang, Y. / James, M.N.G. / Weiner, J.H. | |||||||||
![]() | ![]() Title: Structure-activity characterization of sulfide:quinone oxidoreductase variants. Authors: Cherney, M.M. / Zhang, Y. / James, M.N. / Weiner, J.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.9 KB | Display | ![]() |
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PDB format | ![]() | 148.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sxiC ![]() 3sy4C ![]() 3syiC ![]() 3sz0C ![]() 3szcC ![]() 3szfC ![]() 3szwC ![]() 3t0kC ![]() 3t14C ![]() 3t2kC ![]() 3t2yC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#1: Protein | Mass: 47798.023 Da / Num. of mol.: 1 / Mutation: C356A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Production host: ![]() ![]() References: UniProt: B7JBP8, bacterial sulfide:quinone reductase |
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#3: Sugar | ChemComp-LMT / |
-Non-polymers , 5 types, 347 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/DCQ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DCQ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||||
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#4: Chemical | ChemComp-DCQ / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 30% PEG 600, 0.1 M bis-tris buffer,0.1 M MgSO4, 0.05% DDM, 2 mM decylubiquinone, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2009 |
Radiation | Monochromator: DCM, Si(111) cryo-cooled first crystal and sagittally bent second Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.7955→50 Å / Num. all: 50553 / Num. obs: 46610 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.7955→1.86 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.83 / Num. unique all: 3202 / Rsym value: 0.749 / % possible all: 64.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.235 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7955→30.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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